The development of the systematic evolution of ligands by exponential enrichment (SELEX) process has allowed the isolation of oligonucleotide sequences (referred as aptamers) with the capacity to recognize various classes of target molecules with high affinity and specificity. At the present time, various analytical aptamer-based formats have been developed as suitable tools for the detection and quantification of numerous targets, possessing many potential advantages over the most popular antibody technology. In this review, the aptamer applicability to the separation, purification and quantification of various analytes by liquid chromatography, capillary electrophoresis and electrochromatography is addressed.